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Biochem 2 > Exam 1 > Flashcards

Exam 1 Flashcards

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0
Q

Major types of nucleic acids

A

DNA - deoxyribonucleic acid

RNA - ribonucleic acid

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1
Q

Fourth group of macromolecules

A

Nucleic Acids

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2
Q

Nucleotides are composed of

A

Sugar (pentose - ribose or deoxyribose)
Nitrogenous bases
Phosphate

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3
Q

A phosphate without a phosphate group

A

Nucleoside

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4
Q

Consists of a nitrogenous base covalently attached to a sugar but without a phosphate group

A

Nucleoside

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5
Q

Adenine nucleoside names and nucleic acids

A

Adenosine —- RNA

Deoxyadenosine—- DNA

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6
Q

Adenine nucleotide names

A

Adenylate —- RNA

Deoxyadenylate —- DNA

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7
Q

Guanine nucleoside names

A

Guanosine —- RNA

Deoxyguanosine —- DNA

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8
Q

Purines

A

Adenine and guanine

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9
Q

Guanine nucleotide names

A

Guanylate — RNA

Deoxyguanylate — DNA

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10
Q

Pyrimidines

A

Cytosine, thymine, uracil

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11
Q

Cytosine nucleoside names

A

Cytidine —- RNA

Deoxycytidine —- DNA

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12
Q

Cytosine nucleotide names

A

Cytidylate —- RNA

Deoxycytidylate —- DNA

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13
Q

Thymine nucleoside names

A

Thymidine —- DNA

Deoxythymidine —– DNA

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14
Q

Thymine nucleotide names and nucleic acids

A

Thymidylate —- DNA

Deoxythymidylate —- DNA

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15
Q

Uracil nucleoside names and nucleic acid

A

Uridine — RNA

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16
Q

Uracil nucleotide names and nucleic acid

A

Uridylate —- RNA

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17
Q

DNA nitrogenous bases

A

Adenine - thymine

Guanine - cytosine

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18
Q

RNA nitrogenous bases

A

Adenine - uracil

Guanine - cytosine

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19
Q

Mono ribonucleoside abbreviations (RNA)

A

AMP
GMP
CMP
UMP

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20
Q

Di ribonucleoside abbreviations

A

ADP
GDP
CDP
UDP

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21
Q

Tri ribonucleoside abbreviations

A

ATP
GTP
CTP
UTP

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22
Q

Mono deoxyribonucleoside abbreviations

A

dAMP
dGMP
dCMP
dTMP

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23
Q

Di deoxyribonucleoside abbreviations

A

dADP
dGDP
dCDP
dTMP

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24
Tri deoxyribonucleoside abbreviations
dATP dGTP dCTP dTTP
25
NMP
One phosphate group attached to sugar and nitrogenous base
26
NDP
Two phosphate group attached to sugar and nitrogenous base
27
NTP
Three phosphate group attached to sugar and nitrogenous base
28
Nucleotides are linked covalently to each other by
Phosphodiester bonds
29
Base pair means we have 2 complimentary bases paired with
Hydrogen bonds
30
Nucleotide polymers (I.e. DNA or RNA) exhibit
Directionality
31
Nucleotide polymers also exhibit
Individuality due to the sequences of the bases
32
Phosphodiester bonds are
Very stable
33
Breaks phosphodiester bonds
Nucleases (endo and exo) RNA - ribonuclease DNA - deoxyribonuclease
34
Within molecule clipping
Endo
35
Clips only end nucleotides
Exo
36
RNA is _______ hydrolyzed under alkaline conditions but ______ is not
Rapidly | DNA
37
DNA is most often found as a ________ _______ molecule, twisted into a ________
Double stranded | Helical
38
The DNA strands are
Anti parallel
39
The two DNA strands that make up dsDNA are
Complimentary
40
The c-g and a-t base pairing allows for
DNA self replication
41
Palindrome
Same at the four corners of two DNA strands
42
Mirror repeat
Mirrored in the same line | First half mirrors second half
43
Hairpin
Middle four base pairs at the top curve, the rest down the sides
44
Play an important role in transcription and translation
Hairpin
45
Cruciform
2 hairpins | Looks like a cross
46
Knot like structures in rubber band example
Supercoiling (not sequence dependent)
47
Supercoiling
Happens in DNA when it splits to replicate | Mechanical stress can break phosphodiester bonds
48
What is transcription?
The synthesis of RNA from DNA template
49
2 daughter cells form __________ at the end of replication
Catenane
50
Catenane
Formed by 2 daughter cells at the end of replication
51
Old central dogma
DNA--> more DNA --> RNA --> Protein
52
New Central Dogma
DNA --> more DNA --> RNA --> DNA (reverse transcription)
53
HIV is
reverse transcriptase virus
54
Information RNA
mRNA
55
Structure RNA
rRNA (makes ribosomes)
56
Adapter RNA
tRNA (covalently linked to one of 20 standard amino acids, 3 base anti-codon, 3 base codon in mRNA)
57
Degeneracy
Different codon sequences code for the same amino acid
58
Sense
The coding strand of DNA but this is not the strand from which RNA is made including mRNA because you want RNA to be a sense strand
59
___________ regions in DNA signal RNA Pol where to bind, how tightly to bind, and how frequently to transcribe an RNA chain
Promoter (can be weak or strong; long or short)
60
_____________ regions in DNA signal RNA Pol to stop transcribing
Terminator
61
Transcription is catalyzed by
RNA polymerase
62
Composed of beta prime, beta, alpha, and sigma units
RNA Pol
63
Functions in promoter recognition and initiation
Sigma
64
Regulatory factors associated with RNA Pol include
P (rho), nusA, Tau (all of these function in termination of transcription)
65
When all the subunits of a multi-subunit enzyme associate with each other
Holoenzyme
66
Holoenzyme
When all the subunits of a multi-subunit enzyme associate with each other
67
When the subunits that are essential for the primary function of a multi-subunit enzyme associate with each other
Core Polymerase RNA : no sigma: the assembly is referred to as the core enzyme or polymerase
68
Core Polymerase RNA
When the subunits that are essential for the primary function of a multi-subunit enzyme associate with each other
69
RNA Pol I
Located in nucleolus and produces pre rRNA
70
RNA Pol II
Located in nucleoplasm and produces mRNA, hnRNA (heterogenous nuclear)
71
RNA Pol III
Located in nuceoplasm and produces pre tRNA, 5S RNA
72
There is only 1 ____ ________ ________ in prokaryotes
RNA Pol Holoenzymes
73
Many but NOT ALL eukaryote genes have the common sequence___________ located about ___ to _____ bases before the transcription site
TaTAAATA 25 to 30 TATA BOX
74
TATA is
a subunit of promoter
75
Certain boxes binds selectively to
the TATA sequence
76
Proteins needed to initiate transcription
TATA box
77
CAAT Box
GGCCAATCT or GGTCAATC: Common sequence located 60 - 80 bases upstream from the transcription start site
78
Transcription and translation occur simultaneously in prokaryotes in the
Cytoplasm of the bacterium
79
Transcription in euk. occurs in the
Nucleus
80
Translation in euk. occurs in the
Cytoplasm (on ribosomes)
81
Large mRNA precursor molecules are synthesized in the
Nucleus
82
Form ribonucleoprotein particles
Large mRNA precursor molecules: these are transported from the nucleus to the cytoplasm
83
Modification
Addition or alteration of existing bases or sugars in RNA
84
Sometimes involves the addition of 1 or more nucleotides
Modification
85
Processing
Phosphodiester bond cleavage and loss of certain nucleotides
86
Examples of post-transcriptional modifications
Capping
87
Capping
During transcription a GMP is added to the 5' end of mRNA, G is methylated at position N-7 followed by methylation of the 1st nucleotide in the initial transcription at the O2 on ribose
88
Facilitates the binding of ribosomes to the mRNA
Capping
89
Has reduced half-life compared to capped mRNA
Uncapped mRNA (prevents exonucleases)
90
Most euk. mRNA associated with a ribosome contain _______ adenine nucleotides on 3' end
50 - 150
91
Not coded for by the DNA template
PolyA tail
92
PolyA tail is added post-transcriptionally by
PolyA polymerase
93
Translation
synthesis of polypeptide chain by a ribosome using information encoded in the bases sequence of mRNA
94
Synthesis of polypeptide chain by a ribosome using information encoded in the bases sequence of mRNA
Translation
95
Translation requires
mRNA, tRNA, amino acids, and ribosomes
96
Translation occurs in the _________ direction along the mRNA
5' to 3' | The resulting polypeptide is assembled N-terminus to C-terminus
97
Start codons
AUG | fMet or Met???
98
Stop codons
UAA, UAG, UGA
99
Bacteria ribosomes
50S + 30S = 70S
100
Euk. ribosomes
60S + 40S = 80S
101
Determined by the speed particles traveling through G force like centrifugation
Sedimentation coefficients
102
Ribosome
Ribonucleoprotein (rRNA + protein) Pro. less proteins Euk. More proteins
103
The nucleotide at the Wobble position
Does NOT base pair strongly at 5' on anticodon
104
Wobble position
Anticodon Arm
105
Contains 2 or 3 D residues at different positions
D arm
106
Anticodon arm
wobble position
107
Variable in size, not present in all tRNA
Extra arm
108
Arms starting left going right
D arm, Wobble Position, Anti-codon arm, Extra arm (not always present), TUC (trident= Pseudouridine) arm, Amino acid arm (at top)
109
Specialized base pair called ___________ which pair WEAKLY with all base pairs
Inosinate ------ WEAKLY
110
Activation of Amino Acids
20 AA, 20 aminoacyl-tRNA synthetases, 32 or more tRNA, APT, Mg 2+
111
Initiation
mRNA, N-fMet-tRNA (N-formalmethionyl-tRNA), 30S ribosomal unit, 50S ribosomal unit, initiation factors IF-1, IF-2, IF-3, GTP, Mg 2+
112
Elongation
Functional 70S ribosome (initiation complex), aminoacyl-tRNA sepcified by codons, elongation factors EF-Tu, EF-Ts, EF-G, GTP, Mg 2+
113
Termination and Release
Termination codon in mRNA, release factors RF-1, RF-2. RF-3
114
Folding and Post-translation processing
Specific enzymes, cofactors, and other components for removal of initiating residues and signal sequences, additional proteolytic processing, modification of terminal residues, and attachment of phosphate, methyl, carboxyl, carbohydrate, or prosthetic groups
115
Translation Step 1:
Coupling of tRNA to amino acids/amino acids activation
116
Amino acids are covalently attached to tRNAs by the enzyme
Aminoacyl-tRNA synthetase
117
Synthetase
catalyzes a reaction with ATP involved
118
Synthase
catalyzes a reaction without ATP
119
E. Coli has 20 different aminoacyl-tRNa synthetases, one for each of the standard amino acids, that
improves reaction efficiency linking correct amino acids
120
2 steps in activation of amino acids
1. The amino acid is activated by ATP to form aminoacyl adenlyate = aminoacyl AMP 2. While the aminoacyl adenylate intermediate is bound to the sythetase it reacts with the correct tRNA to form a covalent linkage with it, AMP is released
121
The amino acid is activated by ATP to form
Aminoacyl adenylate = aminoacyl AMP
122
The synthestase _______ choose the correct tRNA based on the anticodon sequence
DOES NOT
123
Critical determinant of choosing the correct tRNA
The sequence in the ACCEPTOR STEM
124
Once tRNA is linked to amino acid, the tRNA is said to be
Charged (not + or -)
125
Process of translation
Ribosome starts process AUG binds on top of P site UAC always carries modified methiamine Once methiamine is in place GTP kicks off initiating factors and allows large subunit to join small Large and small subunit and fMet carrying incoming tRNAs associate with EF-Tu The peptidyl transferase activity of large subunit catalyzes between amino acids Dipeptidyl tRNA forms at the A site Deacylated tRNA Translocation occurs UAG--> Stop codon -->A site RF binds and triggers disassembly of everything and large and subunits separate and empty tRNA is released Cylce repeats
126
Ribosome Cycling
two subunits join and separate repeatedly
127
Helps guide tRNA into ribosome
Elongation factor Tu (EF-Tu)
128
Translocation
Forced movement of mRNA inside ribosome | Can be promoted by GTP
129
Translation occurs on free ribosomes in the cytosol or on ribosomes bound to the ER (rough) in
Eukaryotes
130
Tend to remain cytosolic (water soluble)
Proteins made on free ribosomes
131
Proteins made on rought ER
hydrophobic
132
Protein targeting
The general mechanism for the sorting and transport of proteins to their proper subcellular location
133
Signal sequence
A short amino acid sequence (23-36 AA long) at the N-terminus of newly made polypeptide It is important in targeting
134
One protein being made at N-terminus end (5'end)
Signal sequence
135
Signal Recognition Particle
Large protein complex that directs the forming polypeptide into the lumen of the ER for processing
136
Purpose of the signal sequence
Direct a free ribosome to ER where signal sequence and ribosome are bound by SRP
137
What is transcription?
The synthesis of RNA from DNA template
138
2 daughter cells form __________ at the end of replication
Catenane
139
Catenane
Formed by 2 daughter cells at the end of replication
140
Old central dogma
DNA--> more DNA --> RNA --> Protein
141
New Central Dogma
DNA --> more DNA --> RNA --> DNA (reverse transcription)
142
HIV is
reverse transcriptase virus
143
Information RNA
mRNA
144
Structure RNA
rRNA (makes ribosomes)
145
Adapter RNA
tRNA (covalently linked to one of 20 standard amino acids, 3 base anti-codon, 3 base codon in mRNA)
146
Degeneracy
Different codon sequences code for the same amino acid
147
Sense
The coding strand of DNA but this is not the strand from which RNA is made including mRNA because you want RNA to be a sense strand
148
___________ regions in DNA signal RNA Pol where to bind, how tightly to bind, and how frequently to transcribe an RNA chain
Promoter (can be weak or strong; long or short)
149
_____________ regions in DNA signal RNA Pol to stop transcribing
Terminator
150
Transcription is catalyzed by
RNA polymerase
151
Composed of beta prime, beta, alpha, and sigma units
RNA Pol
152
Functions in promoter recognition and initiation
Sigma
153
Regulatory factors associated with RNA Pol include
P (rho), nusA, Tau (all of these function in termination of transcription)
154
When all the subunits of a multi-subunit enzyme associate with each other
Holoenzyme
155
Holoenzyme
When all the subunits of a multi-subunit enzyme associate with each other
156
When the subunits that are essential for the primary function of a multi-subunit enzyme associate with each other
Core Polymerase RNA : no sigma: the assembly is referred to as the core enzyme or polymerase
157
Core Polymerase RNA
When the subunits that are essential for the primary function of a multi-subunit enzyme associate with each other
158
RNA Pol I
Located in nucleolus and produces pre rRNA
159
RNA Pol II
Located in nucleoplasm and produces mRNA, hnRNA (heterogenous nuclear)
160
RNA Pol III
Located in nuceoplasm and produces pre tRNA, 5S RNA
161
There is only 1 ____ ________ ________ in prokaryotes
RNA Pol Holoenzymes
162
Many but NOT ALL eukaryote genes have the common sequence___________ located about ___ to _____ bases before the transcription site
TaTAAATA 25 to 30 TATA BOX
163
TATA is
a subunit of promoter
164
Certain boxes binds selectively to
the TATA sequence
165
Proteins needed to initiate transcription
TATA box
166
CAAT Box
GGCCAATCT or GGTCAATC: Common sequence located 60 - 80 bases upstream from the transcription start site
167
Transcription and translation occur simultaneously in prokaryotes in the
Cytoplasm of the bacterium
168
Transcription in euk. occurs in the
Nucleus
169
Translation in euk. occurs in the
Cytoplasm (on ribosomes)
170
Large mRNA precursor molecules are synthesized in the
Nucleus
171
Form ribonucleoprotein particles
Large mRNA precursor molecules: these are transported from the nucleus to the cytoplasm
172
Modification
Addition or alteration of existing bases or sugars in RNA
173
Sometimes involves the addition of 1 or more nucleotides
Modification
174
Processing
Phosphodiester bond cleavage and loss of certain nucleotides
175
Examples of post-transcriptional modifications
Capping
176
Capping
During transcription a GMP is added to the 5' end of mRNA, G is methylated at position N-7 followed by methylation of the 1st nucleotide in the initial transcription at the O2 on ribose
177
Facilitates the binding of ribosomes to the mRNA
Capping
178
Has reduced half-life compared to capped mRNA
Uncapped mRNA (prevents exonucleases)
179
Most euk. mRNA associated with a ribosome contain _______ adenine nucleotides on 3' end
50 - 150
180
Not coded for by the DNA template
PolyA tail
181
PolyA tail is added post-transcriptionally by
PolyA polymerase
182
Translation
synthesis of polypeptide chain by a ribosome using information encoded in the bases sequence of mRNA
183
Synthesis of polypeptide chain by a ribosome using information encoded in the bases sequence of mRNA
Translation
184
Translation requires
mRNA, tRNA, amino acids, and ribosomes
185
Translation occurs in the _________ direction along the mRNA
5' to 3' | The resulting polypeptide is assembled N-terminus to C-terminus
186
Start codons
AUG | fMet or Met???
187
Stop codons
UAA, UAG, UGA
188
Bacteria ribosomes
50S + 30S = 70S
189
Euk. ribosomes
60S + 40S = 80S
190
Determined by the speed particles traveling through G force like centrifugation
Sedimentation coefficients
191
Ribosome
Ribonucleoprotein (rRNA + protein) Pro. less proteins Euk. More proteins
192
The nucleotide at the Wobble position
Does NOT base pair strongly at 5' on anticodon
193
Wobble position
Anticodon Arm
194
Contains 2 or 3 D residues at different positions
D arm
195
Anticodon arm
wobble position
196
Variable in size, not present in all tRNA
Extra arm
197
Arms starting left going right
D arm, Wobble Position, Anti-codon arm, Extra arm (not always present), TUC (trident= Pseudouridine) arm, Amino acid arm (at top)
198
Specialized base pair called ___________ which pair WEAKLY with all base pairs
Inosinate ------ WEAKLY
199
Activation of Amino Acids
20 AA, 20 aminoacyl-tRNA synthetases, 32 or more tRNA, APT, Mg 2+
200
Initiation
mRNA, N-fMet-tRNA (N-formalmethionyl-tRNA), 30S ribosomal unit, 50S ribosomal unit, initiation factors IF-1, IF-2, IF-3, GTP, Mg 2+
201
Elongation
Functional 70S ribosome (initiation complex), aminoacyl-tRNA sepcified by codons, elongation factors EF-Tu, EF-Ts, EF-G, GTP, Mg 2+
202
Termination and Release
Termination codon in mRNA, release factors RF-1, RF-2. RF-3
203
Folding and Post-translation processing
Specific enzymes, cofactors, and other components for removal of initiating residues and signal sequences, additional proteolytic processing, modification of terminal residues, and attachment of phosphate, methyl, carboxyl, carbohydrate, or prosthetic groups
204
Translation Step 1:
Coupling of tRNA to amino acids/amino acids activation
205
Amino acids are covalently attached to tRNAs by the enzyme
Aminoacyl-tRNA synthetase
206
Synthetase
catalyzes a reaction with ATP involved
207
Synthase
catalyzes a reaction without ATP
208
E. Coli has 20 different aminoacyl-tRNa synthetases, one for each of the standard amino acids, that
improves reaction efficiency linking correct amino acids
209
2 steps in activation of amino acids
1. The amino acid is activated by ATP to form aminoacyl adenlyate = aminoacyl AMP 2. While the aminoacyl adenylate intermediate is bound to the sythetase it reacts with the correct tRNA to form a covalent linkage with it, AMP is released
210
The amino acid is activated by ATP to form
Aminoacyl adenylate = aminoacyl AMP
211
The synthestase _______ choose the correct tRNA based on the anticodon sequence
DOES NOT
212
Critical determinant of choosing the correct tRNA
The sequence in the ACCEPTOR STEM
213
Once tRNA is linked to amino acid, the tRNA is said to be
Charged (not + or -)
214
Process of translation
Ribosome starts process AUG binds on top of P site UAC always carries modified methiamine Once methiamine is in place GTP kicks off initiating factors and allows large subunit to join small Large and small subunit and fMet carrying incoming tRNAs associate with EF-Tu The peptidyl transferase activity of large subunit catalyzes between amino acids Dipeptidyl tRNA forms at the A site Deacylated tRNA Translocation occurs UAG--> Stop codon -->A site RF binds and triggers disassembly of everything and large and subunits separate and empty tRNA is released Cylce repeats
215
Ribosome Cycling
two subunits join and separate repeatedly
216
Helps guide tRNA into ribosome
Elongation factor Tu (EF-Tu)
217
Translocation
Forced movement of mRNA inside ribosome | Can be promoted by GTP
218
Translation occurs on free ribosomes in the cytosol or on ribosomes bound to the ER (rough) in
Eukaryotes
219
Tend to remain cytosolic (water soluble)
Proteins made on free ribosomes
220
Proteins made on rought ER
hydrophobic
221
Protein targeting
The general mechanism for the sorting and transport of proteins to their proper subcellular location
222
Signal sequence
A short amino acid sequence (23-36 AA long) at the N-terminus of newly made polypeptide It is important in targeting
223
One protein being made at N-terminus end (5'end)
Signal sequence
224
Signal Recognition Particle
Large protein complex that directs the forming polypeptide into the lumen of the ER for processing
225
Purpose of the signal sequence
Direct a free ribosome to ER where signal sequence and ribosome are bound by SRP
226
Tm
Temperature at which a molecule of DNA is 50% denatured. | Dependent on base composition of DNA
227
Nick
A missing phosphodiester bond. Sealed by DNA ligase
228
Tm
The point at which a molecule is 50% denatured
229
Tm
The point at which a molecule is 50% denatured

Biochem 2 (3 decks)

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